Optimizes biomarker selection for cost-effective treatment rules.
problem Incorporating multiple biomarkers in treatment selection rules can be costly and reduce model performance.
method Developed procedures for estimating linear and nonlinear combinations of biomarkers using 0-norm penalized weighted classification.
result Demonstrated the importance of feature selection and marker cost in treatment selection rules.
This paper compares feature selection methods for biomarker discovery in toxicant-treated fish.
problem Choosing the most suitable method for biomarker discovery in toxicant exposure studies.
method Three feature selection methods: SAM, mRMR, and GeoDE are compared.
result Different methods perform better in different cases, requiring dataset-specific decisions.
New methods use network data to find genetic indicators for diseases.
problem Finding genetic indicators for diseases from large, complex data.
method Integrating network data to select features from whole-genome data.
result Methods can identify genetic indicators that work together.
A method for biomarker selection using aggregated data under data protection constraints.
problem Manual data exchange and limited data calls hinder joint analyses of clinical biomarkers.
method Distributed multivariate regression modeling for automatic variable selection.
result The heuristic variant reduces data calls from over 10 to 3, making manual data releases feasible.
Flexible variable selection handles missing data for better biomarker panels.
problem Identifying relevant features from incomplete data sets.
method Nonparametric variable selection combined with multiple imputation.
result Improved biomarker panels with higher classification and variable selection performance.
ROOFS helps researchers select robust biomarker features from complex data.
problem Challenges in feature selection for biomarker discovery and clinical models.
method ROOFS is a Python package that benchmarks multiple feature selection methods on user data.
result ROOFS identifies a filter method as optimal for identifying predictors of lung cancer resistance.
RIF prioritizes predictive biomarkers for precision medicine.
problem Lack of tools to select and prioritize predictive biomarkers.
method Random Interaction Forest (RIF) method.
result RIF outperformed conventional methods in various simulation scenarios and clinical trials.
PR-GNN identifies salient brain regions for ASD biomarkers.
problem Identifying brain regions associated with neurological disorders.
method Pooling Regularized Graph Neural Network (PR-GNN) with novel salient region selection.
result PR-GNN outperforms baseline methods in ASD classification accuracy.
Feature selection is among the most important components because it not only helps enhance the classification accuracy, but also or even more important provides potential biomarker discovery. However, traditional multivariate methods is likely to obtain unstable and unreliable results in case of an extremely high dimen…
Bayesian Cox model identifies biomarkers from multi-omics data.
problem Produce interpretable survival prognosis from multi-omics data.
method Penalized semiparametric Bayesian Cox model with graph-structured selection priors.
result Model identifies new biomarkers and improves survival prediction.
New method identifies predictive biomarkers for subgroup analysis.
problem Identifying predictive biomarkers from large covariates.
method Generalized penalized regression with overlapped group penalties.
result Asymptotically consistent method for sparse, interpretable models.
AFTNet uses a network-constrained Weibull model for biomarker discovery.
problem Discovering biomarkers from survival data with correlated predictors.
method Survival analysis method based on Weibull AFT model, incorporating network constraints and penalized likelihood for variable selection.
result Theoretical consistency and efficient algorithm for AFTNet estimator validated on synthetic and real data.
Proposes ConRad model for lung cancer classification using radiomics and interpretable machine learning.
problem Lack of interpretability in deep neural networks for cancer diagnosis.
method Integration of radiomics and DNN-predicted biomarkers in interpretable classifiers (ConRad).
result ConRad models outperform CNNs in five-fold cross-validation.
Bayesian model tackles mixed-type data challenges.
problem Challenges in EM algorithm sensitivity, biomarker LOD, and variable importance.
method Bayesian finite mixture model with variable selection, LOD handling, and spike-and-slab prior.
result Improved parameter estimates and variable importance.
RobKMR improves robustness in multi-omics data analysis for osteoporosis biomarker discovery.
problem Sensitivity to adversarial outliers and lack of comprehensive multi-omics data integration.
method RobKMR, a non-linear M-estimator-based approach using robust kernel centered Gram matrix and robust score test.
result Selected biomarkers (DKK1, MTND5, FASTKD2) significantly bond with four drugs for osteoporosis.
The study compares feature learning techniques for predicting Alzheimer's disease from MRI.
problem Predicting cognitive impairment from MRI data.
method Review and comparison of feature learning and selection techniques.
result Stacked auto-encoders outperformed other methods in MRI-based Alzheimer's disease prediction.
A new framework models multi-state events and biomarkers.
problem Limited representation of complex multi-state trajectories.
method General multi-state joint modeling framework.
result Accurate parameter recovery and personalized predictions.
The study ranks biomarkers using mutual information, tackling clinical trial challenges.
problem Disentangling predictive and prognostic biomarkers in clinical trials.
method Formalizing biomarker ranking as optimizing mutual information, estimating conditional mutual information terms with efficient approximations and empirical Bayes, introducing a visualisation tool.
result Efficient methods to rank predictive and prognostic biomarkers, visualisation tool for biomarker discovery.
Transformers improve Alzheimer's disease progression prediction by accounting for irregular biomarker histories.
problem Difficult prediction of medium-horizon Alzheimer's disease progression due to tied clinical scores and irregular biomarker observations.
method Developed a residual gap-aware transformer that combines statistical reference with transformer-based residual learning.
result The proposed model reduces mean error and improves prediction-observation correlation compared to baseline models.
OBF optimally filters features under independent Gaussian models.
problem Biomarker discovery from complex data.
method Optimal Bayesian feature selection under independent Gaussian models.
result OBF is consistent and optimal under mild conditions.
Study uses machine learning to identify IBD biomarkers from gut microbiota.
problem Identifying biomarkers for Inflammatory Bowel Disease (IBD) from gut microbiota.
method Ensemble feature selection methods (CMIM, FCBF, mRMR, XGBoost) applied to IBD-associated metagenomics dataset.
result XGBoost minimizes microbiota used for IBD diagnosis, improving classification accuracy.
New method detects biomarker-treatment interactions in clinical trials.
problem Detecting interactions between high-dimensional biomarkers and treatments in randomized trials.
method Two-stage penalized regression screening using ridge regression for multivariate screening.
result Ridge regression screening provides greater power than traditional methods in correlated data.
Study finds PLI functional connectivity feature superior for depression recognition.
problem Effective detection of depression remains a public health challenge.
method Resting state EEG data collected from MDD and normal controls; various feature types and selection methods evaluated.
result PLI functional connectivity feature superior to linear and nonlinear features; highest classification accuracy 82.31%.
AdapDISCOM tackles high-dimensional multimodal data with missingness and errors, improving prediction and biomarker selection.
problem High-dimensional multimodal data with block-wise missingness and measurement errors.
method AdapDISCOM introduces modality-specific weighting schemes to address heterogeneity and error magnitudes.
result AdapDISCOM consistently outperforms existing methods under heterogeneous contamination and heavy-tailed distributions.
A method to explain disease transformation using biomarker covariance matrices.
problem Understanding disease transformation from a healthy baseline.
method Modeling healthy and disease states of biomarker covariance matrices to characterize perturbations.
result Disease perturbs the biomarker covariance structure, allowing for mechanistic explanations and individual patient prognosis.
Neural network models improve ROC curve evaluation of biomarkers, focusing on age's role in physical activity-mortality association.
problem Improving biomarker evaluation using machine learning for complex relationships.
method Proposes neural network-based covariate-adjusted ROC modeling.
result Age has distinct effects on mortality outcomes when physical activity is measured as total activity time.
The development of molecular signatures for the prediction of time-to-event outcomes is a methodologically challenging task in bioinformatics and biostatistics. Although there are numerous approaches for the derivation of marker combinations and their evaluation, the underlying methodology often suffers from the proble…
New biomarker predicts MRgFUS treatment outcome without contrast agents.
problem Inaccurate assessment of treated tissue viability after MRgFUS.
method Deep learning on noncontrast multiparametric MRI images, voxel-wise registration.
result Predicted follow-up NPV with DICE coefficient 0.71, outperforming current standard.
Super-resolution improves MRI resolution and accuracy for biomarker assessment.
problem Inadequate SNR for accurate quantification in high-resolution MRI.
method Utilized deep learning super-resolution to maintain SNR for T2 relaxation time biomarkers while generating high-resolution images.
result Super-resolution successfully maintains high-resolution and accurate biomarkers for MRI.
Machine learning improves glioma diagnosis and prognosis.
problem Improving glioma diagnosis and prognosis using imaging biomarkers.
method Search PubMed and MEDLINE for articles applying machine learning to high-grade glioma biomarkers.
result Machine learning enables accurate classification of glioma biomarkers.
Gaussian OBFS proves strong consistency in feature selection with correlations.
problem Feature selection consistency in the presence of correlations.
method Proves strong consistency of Gaussian OBFS under mild conditions.
result Identifies selected features and rates of convergence for different feature types.
Graph Neural Network identifies ASD biomarkers from fMRI data.
problem Finding biomarkers for Autism Spectrum Disorder (ASD).
method Graph Neural Network (GNN) for analyzing task-fMRI brain networks, 2-stage pipeline to interpret feature importance.
result GNN achieves high accuracy in identifying ASD biomarkers and reveals their association with social behaviors.
DKT transfers biomarker information between neurodegenerative diseases.
problem Estimating biomarker trajectories in rare neurodegenerative diseases with limited data.
method DKT is a joint-disease generative model that transfers biomarker progressions from common neurodegenerative diseases to rare ones.
result DKT estimates plausible multimodal biomarker trajectories in rare diseases like PCA using only unimodal data.
New method handles correlated genes for better genomic prediction.
problem Technical issues with highly correlated genes in prediction models.
method Grouping algorithm that treats correlated genes as a group and uses their common patterns.
result Significantly outperforms standard models in prediction and feature selection.
This research uses cooperative game theory to interpret deep learning models for ASD biomarker discovery.
problem Understanding image features used by deep learning models for ASD biomarker discovery.
method Shapley value explanation (SVE) from cooperative game theory applied to deep learning models with graph structure optimization.
result SVE provides more accurate biomarker importance than traditional methods.
Motivation: Biomarker discovery from high-dimensional data is a crucial problem with enormous applications in biology and medicine. It is also extremely challenging from a statistical viewpoint, but surprisingly few studies have investigated the relative strengths and weaknesses of the plethora of existing feature sele…
Method predicts biomarker trajectories with uncertainty bands for Alzheimer's disease.
problem Uncertainty in biomarker predictions poses risks in clinical deployment.
method Conformal prediction for randomly-timed biomarker trajectories.
result Conformal bands achieve desired coverage and are tighter than baseline.
EBM uses high-dimensional imaging biomarkers to improve dementia progression estimation.
problem Current EBMs only use scalar biomarkers, limiting accuracy from cross-sectional data.
method Proposes nDEBM, a novel method using semi-supervised SVM on voxel-wise imaging biomarkers.
result nDEBM outperforms state-of-the-art EBM methods using regional volume biomarkers.
Study identifies biomarkers for lung cancer in female non-smokers.
problem Identifying prognostic biomarkers for stage III NSCLC in non-smoking females.
method Gene expression profiling and XGBoost machine learning algorithm.
result Top biomarkers validated in literature, with AUC score of 0.835.
Novel framework predicts brain biomarker trajectories with superior performance.
problem Challenges in estimating longitudinal brain biomarker trajectories due to variability, inconsistencies, and irregular measurements.
method Personalized deep kernel regression with Adaptive Shrinkage Estimation.
result Superior predictive performance compared to state-of-the-art models.
Background: Predictive, stable and interpretable gene signatures are generally seen as an important step towards a better personalized medicine. During the last decade various methods have been proposed for that purpose. However, one important obstacle for making gene signatures a standard tool in clinics is the typica…
engGNN combines external and generated graphs to improve disease classification and biomarker discovery.
problem Challenges in integrating omics data due to high dimensionality and small sample sizes.
method Dual-graph framework that integrates external biological networks with data-driven generated graphs.
result engGNN outperforms state-of-the-art methods in disease classification and biomarker discovery.
New method uses SHAP for biomarker identification in CATE models.
problem Identifying predictive biomarkers from observational data.
method Surrogate estimation approach using SHAP values for CATE meta-learners.
result SHAP accurately identifies biomarkers in high-dimensional data.
Develops a feature selection method for multi-view data with mixed types.
problem Challenges in feature selection for high-dimensional multi-view data with mixed data types.
method Block Randomized Adaptive Iterative Lasso (B-RAIL) combining randomized Lasso, adaptive weighting, and stability selection.
result Demonstrates effectiveness of B-RAIL in identifying biomarkers and novel candidates for ovarian cancer.
FRI identifies relevant features in high-dimensional data for biomedical experiments.
problem Spurious feature selection in high-dimensional data.
method Feature relevance method for identifying all-relevant variables in linear classification and regression.
result FRI can identify causal features in biomedical experiments.
New biomarkers for autism detected from R-fMRI data.
problem Challenges in extracting functional biomarkers from multi-site R-fMRI data for complex neuropsychiatric disorders.
method Developed pipelines to extract participant-specific connectomes from functionally-defined brain areas, compared across participants, and predicted neuropsychiatric status.
result 67% prediction accuracy on ABIDE dataset, significantly better than previous results.
New method integrates network knowledge for better clinical risk prediction and biomarker discovery.
problem Improving predictive ability and interpretability of biomarkers using molecular profiling data.
method Introduces a network-regularized sparse Logistic Regression framework with a new penalty term.
result Demonstrates improved performance in simulated and real data compared to existing methods.
In this paper, we consider voxel selection for functional Magnetic Resonance Imaging (fMRI) brain data with the aim of finding a more complete set of probably correlated discriminative voxels, thus improving interpretation of the discovered potential biomarkers. The main difficulty in doing this is an extremely high di…